KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti- Phospho-tau (Ser202, Thr205) (AT8), biotinylated | Thermo Fisher Scientific | Cat# MN1020B, RRID: AB_223648 |
| Mouse monoclonal anti-human tau (HT7), biotinylated | Thermo Fisher Scientific | Cat# MN1000B, RRID: AB_223453 |
| Rabbit polyclonal anti-Synapsin 1 | Synaptic Systems | Cat# 106103, RRID: AB_11042000 |
| Rat monoclonal anti-CD68, clone FA-11 | AbD SeroTec | Cat# MCA1957 |
| Rabbit polyclonal anti-GFAP (GFAP) | Abcam | Cat# ab7260, RRID: AB_305808 |
| Mouse monoclonal anti-p-tau HJ14.5 (Thr181) | In house (Shi et al., 2019) | N/A |
| Mouse monoclonal anti-tau (TAU-5) | Gift from L. Binder, Northwestern University (LoPresti et al., 1995) | N/A |
| Mouse monoclonal anti-apoE HJ6.2 | In house (Kim et al., 2012) | N/A |
| Mouse monoclonal anti-murine apoE HJ6.8, biotinylated | In house (Liao et al., 2015) | N/A |
| Mouse monoclonal anti-murine apoE HJ6.3 | In house (Kim et al., 2012) | N/A |
| APC-Cy7 rat anti-CD11b (clone M1/70) | BD Biosciences | Cat# 557657, RRID: AB_396772 |
| BV421 Rat Anti-Mouse CD24 (clone M1/69) | BD Biosciences | Cat# 562563, RRID: AB_2737002 |
| ACSA2-PE | Miltenyi Biotec | Cat# 130-123-284, RRID: AB_2811488 |
| O4-APC | Miltenyi Biotec | Cat# 130-118-978, RRID: AB_2751598 |
| Rabbit polyclonal anti-NG2 (CSPG4) | Sigma-Aldrich | Cat# AB5320, RRID: AB_11213678 |
| Mouse monoclonal anti-α-tubulin | Sigma-Aldrich | Cat# T5168, RRID: AB_477579 |
| Rabbit monoclonal anti-LDLR (EP1553Y) | Abcam | Cat# ab52818, RRID: AB_881213 |
| Rabbit polyclonal anti Iba1 | Wako | Cat# 019-19741, RRID: AB_839504 |
| Goat Polyclonal anti-LDLR | R&D Systems | Cat# AF2255, RRID: AB_355203 |
| Mouse monoclonal anti- Legumain (B-8) | Santa Cruz Biotechnology | Cat# sc-133234, RRID: AB_2135017 |
| Mouse monoclonal anti Vimentin (E-5) | Santa Cruz Biotechnology | Cat# sc-373717, RRID: AB_10917747 |
| Rabbit monoclonal anti-Phospho-4E-BP1 (Thr37/46) (236B4) | Cell Signaling Technology | Cat# 2855, RRID: AB_560835 |
| Rabbit polyclonal anti- Myelin Basic Protein | Abcam | Cat# ab40390 RRID: AB_1141521 |
| Rabbit monoclonal anti-Pan-Actin (D18C11) | Cell Signaling Technology | Cat# 8456, RRID: AB_10998774 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Sudan Black B | Sigma-Aldrich | Cat# 199664 |
| DMEM, high glucose | Gibco | Cat# 11965084 |
| Fetal Bovine Serum, qualified, USDA-approved regions | Gibco | Cat# 10437028 |
| Penicillin-Streptomycin (10,000 U/mL) | Gibco | Cat# 15140122 |
| GlutaMAX™ Supplement | Gibco | Cat# 35050061 |
| Poly-L-lysine hydrobromide | Sigma-Aldrich | Cat# P2636 |
| MEM Non-Essential Amino Acids Solution (100X) | Gibco | Cat# 11140050 |
| DMEM/F-12, HEPES, no phenol red | Gibco | Cat# 11039021 |
| Insulin-Transferrin-Selenium (ITS -G) (100X) | Gibco | Cat# 41400045 |
| B-27 Supplement (50X), minus vitamin A | Gibco | Cat# 12587010 |
| N-2 Supplement (100X) | Gibco | Cat# 17502048 |
| 1-Thioglycerol | Sigma-Aldrich | Cat# M1753 |
| Insulin solution human | Sigma-Aldrich | Cat# I9278 |
| Recombinant Human TGF-beta 1 Protein | R&D Systems | Cat# 240-B |
| Recombinant Human IL-34 Protein | R&D Systems | Cat# 5265-IL |
| Recombinant Human M-CSF Protein | R&D Systems | Cat# 216-MC |
| 4-Methylumbelliferyl-β-D-glucuronide hydrate (β-Gluc substrate) | Sigma-Aldrich | Cat# M9130 |
| 4-Methylumbelliferyl-6-sulfo-N-acetyl-β-D-glucosaminide (Hexa substrate) | Sigma-Aldrich | Cat# 454428 |
| 4-Methylumbelliferyl N-acetyl-β-D-glucosaminide (Naglu Substrate) | Sigma-Aldrich | Cat# M2133 |
| Mouse BD Fc Block | BD Biosciences | Cat# 553141 |
| Brilliant stain buffer | BD Biosciences | Cat# 563794 |
| 4-Methylumbelliferone | Sigma-Aldrich | Cat# M1381 |
| Critical Commercial Assays | ||
| VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) | Vector laboratories | Cat# PK-6100 |
| Micro BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23235 |
| Neural Tissue Dissociation Kit (T) | Miltenyi Biotec | Cat# 130-093-231 |
| Adult Brain Dissociation Kit | Miltenyi Biotec | Cat# 130-107-677 |
| RNeasy Mini Kit | QIAGEN | Cat# 74104 |
| Nuclei Isolation Kit: Nuclei PURE Prep | Sigma-Aldrich | Cat# NUC201 |
| RNA-to-cDNA kit | Applied Biosystems | Cat# 4387406 |
| DC Protein Assay Kit I | BIO-RAD | Cat# 5000111 |
| Deposited Data | ||
| snRNAseq raw data | This paper | GEO accession number GSE166261 |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6/C3-Tg (Prnp-MAPT*P301S) PS19Vle/J, crossed to B6 background | The Jackson Laboratory | Cat# 008169 |
| Mouse: Ldlr Tg | (Kim et al., 2009) | N/A |
| Mouse: B6.129P2-Apoetm1Unc/J | The Jackson Laboratory | Cat# 002052 |
| Mouse: C57BL/6NCrl WT | Charles River Laboratories | Cat# 027 |
| Oligonucleotides | ||
| Taqman qPCR primers for Gabra6 | Thermo Fisher Scientific | ID: Mm01227754_m1 |
| Taqman qPCR primers for Grm4 | Thermo Fisher Scientific | ID: Mm01306128_m1 |
| Taqman qPCR primers for Apoe | Thermo Fisher Scientific | ID: Mm01307193_g1 |
| Taqman qPCR primers for Lilrb4 | Thermo Fisher Scientific | ID: Mm01614371_m1 |
| Taqman qPCR primers for Spp1 | Thermo Fisher Scientific | ID: Mm00436767_m1 |
| Taqman qPCR primers for Il1b | Thermo Fisher Scientific | ID: Mm00434228_m1 |
| Taqman qPCR primers for Ldlr | Thermo Fisher Scientific | ID: Mm01177349_m1 |
| Taqman qPCR primers for Lgmn | Thermo Fisher Scientific | ID: Mm01325350_m1 |
| Taqman qPCR primers for Actb | Thermo Fisher Scientific | ID: Mm01205647_g1 |
| Software and Algorithms | ||
| Prism 8 | GraphPad | https://www.graphpad.com/ |
| ImageJ 1.52p | ImageJ | https://imagej.net/Fiji |
| FlowJo v10 | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo/downloads |
| Cell Ranger Single-Cell Software Suite | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| Seurat v2 | (Butler et al., 2018) | https://satijalab.org/seurat/articles/install.html |
| R 2.4.0 (for snRNAseq analysis) | R foundation | https://cran-archive.r-project.org/bin/windows/base/old/2.4.0/ |
| Metascape | Metascape | https://metascape.org/gp/index.html#/main/step1 |